@SpookiLurkr It could be that I'm just not well-read enough to have encountered more of them, but I think one of the reasons that stories focused around imaginary friends can be somewhat difficult to find is because, in many cultures, the concept of an imaginary friend is considered inherently childish, and something that should be relinquished as early as possible, so by the time many find the passion for writing, film, or whatever medium they might prefer, the very idea of an imaginary friend is such a distant memory to them that it doesn't factor into their thoughts or work.
That said, I do have two examples that somewhat skew in that direction, though they're both somewhat iffy examples. One being
Kurayami Dance. Written by Goichi Suda, (in)famous for his heavy use of mindscrew in his games, this manga was essentially the initial concept for what eventually became the game Shadows of the Damned. If you read this side-by-side with the game, you can see some of the influences from Kurayami Dance still present in the finished product, even though the end result was ultimately something wholly different. While absolutely not the main focus of the story, the main character DOES have something of an imaginary friend whose presence is vital to at least one of the mysteries in the story, and tags along with them for a good chunk of the journey.
The other is
Mayonaka Sanpo by Nekonome Hideo. The story doesn't explicit spell out that the main character's companion is imaginary, but given the context of the story, it's not hard to draw the conclusion that they are, in fact, a product of the MC's imagination.
I apologize if this isn't quite what you were looking for, but I still recommend both manga for their quality, if nothing else.
For a non-manga medium, there's always the movie Fight Club.
I'll see myself out.
